Light Activation of Staphylococcus aureus Toxin YoeBSa1 Reveals

Nov 26, 2013 - the antitoxin counteracts the activity of the toxin.2−4 In Type II. TA systems, the antitoxin is a protein that binds to the toxin an...
0 downloads 0 Views 3MB Size
Download PDF
Article pubs.acs.org/biochemistry

Light Activation of Staphylococcus aureus Toxin YoeBSa1 Reveals Guanosine-Specific Endoribonuclease Activity Amy S. Larson and Paul J. Hergenrother* Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States S Supporting Information *

ABSTRACT: The Staphylococcus aureus chromosome harbors two homologues of the YefM-YoeB toxin−antitoxin (TA) system. The toxins YoeBSa1 and YoeBSa2 possess ribosomedependent ribonuclease (RNase) activity in Escherichia coli. This activity is similar to that of the E. coli toxin YoeBEc, an enzyme that, in addition to ribosome-dependent RNase activity, possesses ribosome-independent RNase activity in vitro. To investigate whether YoeBSa1 is also a ribosome-independent RNase, we expressed YoeBSa1 using a novel strategy and characterized its in vitro RNase activity, sequence specificity, and kinetics. Y88 of YoeBSa1 was critical for in vitro activity and cell culture toxicity. This residue was mutated to o-nitrobenzyl tyrosine (ONBY) via unnatural amino acid mutagenesis. YoeBSa1Y88ONBY could be expressed in the absence of the antitoxin YefMSa1 in E. coli. Photocaged YoeBSa1-Y88ONBY displayed UV light-dependent RNase activity toward free mRNA in vitro. The in vitro ribosome-independent RNase activity of YoeBSa1Y88ONBY, YoeBSa1-Y88F, and YoeBSa1-Y88TAG was significantly reduced or abolished. In contrast to YoeBEc, which cleaves RNA at both adenosine and guanosine with a preference for adenosine, YoeBSa1 cleaved mRNA specifically at guanosine. Using this information, a fluorometric assay was developed and used to determine the kinetic parameters for ribosome-independent RNA cleavage by YoeBSa1.

T

chromosomally encoded TA systems is somewhat controversial, with at least 13 proposed roles, including junk DNA, selfish genes, stabilization of mobile genetic elements, anti-addiction elements, gene regulation, growth control/stress response, persistence, growth arrest, programmed cell death, phage defense, biofilm formation, virulence, and phenotypic bistability.8,9 However, it is generally accepted that cellular stress modulates transcription at the TA locus and stimulates degradation of the antitoxin, releasing the toxin to act on its cellular target and arrest growth until conditions become more favorable.5 Upon the cessation of stress, the antitoxin is replenished, inactivating the toxin and allowing the cell to resume normal growth.10 The growth arrest and eventual cell death resulting from toxin overexpression have led to the proposal that artificial toxin activation could provide an effective antibacterial strategy.11−14 The Gram-positive pathogen Staphylococcus aureus is the leading cause of bloodstream, lower respiratory tract, and skin and soft tissue infections worldwide.15 A recent comparative genomic analysis identified between one and seven Type II TA loci in the sequenced genomes of 14 S. aureus strains, including YefM-YoeBSa1 and YefM-YoeBSa2 (previously identified as Axe1-Txe1 and Axe2-Txe2, respectively)16,17 that are homologues of the YefM-YoeBEc TA system from Escherichia coli.18 The toxin YoeBEc possesses ribosome-independent RNase

oxin−antitoxin (TA) systems are genetic modules that are found in almost all free-living prokaryotes.1 TA loci encode a protein toxin and a protein or RNA antitoxin and are grouped into five types on the basis of the mechanism by which the antitoxin counteracts the activity of the toxin.2−4 In Type II TA systems, the antitoxin is a protein that binds to the toxin and prevents it from interacting with its cellular target. The activity of Type II toxins is regulated by the differential susceptibility of the toxin and the antitoxin to proteolysis. The antitoxin is more labile than the toxin and must be continuously expressed to maintain cellular levels capable of inhibiting the toxin. Toxin inhibition is relieved by the activity of cellular proteases, which degrade the labile antitoxin and shift the antitoxin:toxin ratio to favor the free toxin, which can then act on its cellular target.5 The targets of TA system toxins include DNA replication, protein translation, and cell wall biosynthesis. Many toxins are ribonucleases (RNases) that inhibit translation by cleaving RNA in a ribosome-dependent or -independent fashion.2 TA systems were originally discovered on plasmids, where they function as a postsegregational killing mechanism to maintain a plasmid in a bacterial population. If a daughter cell inherits a plasmid containing a TA locus during replication, both the antitoxin and the toxin will be expressed to form a stable, innocuous complex, and the cell will survive. However, if the plasmid is not inherited, rapid proteolytic degradation of the antitoxin will release the toxin to act on its cellular target and kill the cell, thereby eliminating plasmid-free cells from the population.6 TA systems were subsequently discovered on the chromosomes of many bacteria and archaea.1,7 The function of © 2013 American Chemical Society

Received: June 22, 2013 Revised: November 26, 2013 Published: November 26, 2013 188

dx.doi.org/10.1021/bi4008098 | Biochemistry 2014, 53, 188−201

Biochemistry

Article

activity in vitro as well as ribosome-dependent RNase activity in vitro and in cells.19,20 YoeBEc binds in the A site of the 50S ribosomal subunit, causing cleavage of mRNA transcripts three bases downstream of the start codon.20 It is unknown whether YoeBEc-mediated mRNA cleavage on the ribosome results from direct catalysis by YoeBEc, from enhancement of the latent ribonucleolytic activity of the ribosome upon binding of YoeBEc, or from some combination of the two.20 A significant challenge when studying toxic proteins is the difficulty associated with their expression and purification in E. coli. Herein, we present a novel solution to this problem by incorporating a noncanonical amino acid, a photocaged tyrosine derivative, to replace a tyrosine that is critical for the activity and toxicity of YoeBSa1. Using protein produced through this method, the substrate specificity of YoeBSa1 was unveiled, allowing the creation of a fluorogenic substrate that can be used to monitor YoeBSa1 activity.

the modification that lysis was performed by vortexing resuspended cells at maximal speed for 5 × 1 min pulses at room temperature with recovery for 1−5 min on ice between pulses. Isolated RNA was treated with DNase I and purified with reagents from the Total RNA Kit I (Omega Bio-Tek) according to the RNA Cleanup protocol from the RNeasy Mini Handbook (Qiagen). Purified total RNA (10 ng) was used in RT-PCR and in PCR with Platinum Taq DNA Polymerase (Invitrogen) to detect DNA contamination. RT-PCR was performed with primers YefM-YoeBSa1-F and YefM-YoeBSa1-R or YefM-YoeBSa2-F and YefM-YoeBSa2-R using the Superscript III One-Step RT-PCR System with Platinum Taq (Invitrogen) as previously reported22 with the following modifications: the annealing temperature was increased to 55 °C, and the number of cycles was reduced to 35. PCR products were separated by electrophoresis on 1% agarose gels and stained with ethidium bromide. Construction of Plasmids. The yoeBSa1 open reading frame (ORF) was amplified via PCR from the total DNA of MRSA S421 with primers YoeBSa1-NdeI-F and YoeBSa1-Y88FHindIII-R or YoeBSa1-Y88TAG-HindIII-R and cloned into the corresponding sites of pET-28a (Novagen) to create pET-28ayoeBSa1-Y88F and pET-28a-yoeBSa1-Y88TAG, respectively. The yef M-yoeBSa1 ORF was amplified via PCR from the total DNA of MRSA S421 with primers YefMSa1-NdeI-F and YoeBSa1HindIII-R and cloned into the corresponding sites of pET-28a. Because a single nonsilent point mutation was found in the sequence for YefMSa1, Quikchange site-directed mutagenesis was performed with primers YefMSa1-QC-F and YefMSa1-QC-R to create pET-28a-yef M-yoeBSa1. Site-directed mutagenesis was carried out with the Quikchange site-directed mutagenesis kit (Stratagene) according to the manufacturer’s instructions with the modification that E. coli DH5α was used as the host strain. The yef MSa1 ORF was amplified via PCR from the total DNA of MRSA NRS3 (Network on Antimicrobial Resistance in S. aureus) with primers YefMSa1-NdeI-F and YefMSa1-XhoI-R and cloned into the corresponding sites of pET-28a to create pET28a-yef MSa1. All clones were confirmed by sequencing. The following antibiotic concentrations were used: 50 μg/mL kanamycin (pET-28a), 35 μg/mL chloramphenicol (pEVOLONBY), and 100 μg/mL ampicillin (Pentaprobes). ONBY Synthesis. o-Nitrobenzyl tyrosine (ONBY) was synthesized according to a previously published method25 with some modifications. Two grams (11 mmol) of L-tyrosine was stirred with 1.9 g (7.6 mmol) of CuSO4·5H2O in 20 mL of 1 M NaOH at 60 °C for 20 min. The reaction was cooled to room temperature, quenched with hydrochloric acid, filtered, and washed with water. The resulting solid was stirred with 1.5 g (11 mmol) of K2CO3 and 1.8 g (8.3 mmol) of o-nitrobenzyl bromide in 60 mL of 75% aqueous dimethylformamide (DMF) at room temperature in the dark for 3 days. The resulting solid was filtered; washed with 75% aqueous DMF, water, 75% aqueous acetone, and ice-cold acetone; stirred in 100 mL of 1 M HCl for 2 h; filtered; stirred in 100 mL of 1 M HCl for 1 h; filtered; and washed with water and acetone. The overall yield was 1.8 g (5.7 mmol, 69%). Purification of YoeBSa1-Y88F and YoeBSa1-Y88TAG. pET-28a-yoeBSa1-Y88F or pET-28a-yoeBSa1-Y88TAG was introduced into E. coli NiCo21(DE3). A single colony from a freshly streaked plate was inoculated into LB medium supplemented with kanamycin and grown at 37 °C with shaking at 250 rpm overnight (14−16 h). The overnight culture was diluted 1:100 and grown at 37 °C with shaking at 250 rpm until the A600

■

EXPERIMENTAL PROCEDURES Bacterial Strains. MRSA clinical isolates were from a previously published collection.21 E. coli DH5α and NiCo21(DE3) were used for cloning and protein expression, respectively. Primers. All primers used for polymerase chain reaction (PCR), reverse transcription PCR (RT-PCR), cloning, and sitedirected mutagenesis were synthesized by Integrated DNA Technologies (IDT) and are listed in Table S1 of the Supporting Information. PCR Analysis of Clinical Isolates. Total DNA was previously purified from a diverse collection of 78 clinical isolates of MRSA.21 Primers YefM-YoeBSa1-F and YefMYoeBSa1-R or YefM-YoeBSa2-F and YefM-YoeBSa2-R were used to amplify the yef M-yoeBSa1 or yef M-yoeBSa2 loci, respectively, from the total DNA. Primers YefMSa1-NdeI-F, YefMSa1-XhoI-R, YoeBSa1-NdeI-F, YoeBSa1-HindIII-R, YefMSa2-NdeI-F, YefMSa2HindIII-R, YoeBSa2-NdeI-F, and YoeBSa2-HindIII-R were used to amplify the yef MSa1, yoeBSa1, yef M-yoeBSa1, yef MSa2, yoeBSa2, and yef M-yoeBSa2 operons from the total DNA of strains NRS27 and NRS76. PCR amplification was performed on a DNA thermocycler using previously described reaction conditions.21,22 PCR products were separated by electrophoresis on 1% agarose gels and stained with ethidium bromide. Sequencing Analysis. Approximately 10% of the PCR products generated via PCR amplification of the yef M-yoeBSa1 and yef M-yoeBSa2 loci were sequenced by the University of Illinois W. M. Keck Center for Comparative and Functional Genomics. Sequence data were analyzed using BioEdit version 7.0.5.3. The sequences were aligned using CLUSTAL W23 and used as query sequences to search the BLAST database to verify the identity of the PCR products and homology to known genes.24 RT-PCR Analysis of Clinical Isolates. MRSA isolates were streaked from glycerol stocks on Brain Heart Infusion (BHI) agar. Single colonies from freshly streaked plates were inoculated into 10 mL of BHI medium and incubated aerobically at 37 °C with shaking at 250 rpm overnight (14− 16 h). Overnight cultures were diluted 1:100 in 10 mL of BHI medium and incubated aerobically at 37 °C with shaking at 250 rpm until the A600 reached 0.6−1.0. Logarithmically growing cultures were harvested by centrifugation at 3220g for 10 min at 4 °C. Total RNA was purified using the FastRNA Pro Blue Kit (Qbiogene) according to the manufacturer’s instructions with 189

dx.doi.org/10.1021/bi4008098 | Biochemistry 2014, 53, 188−201

Biochemistry

Article

ESI-MS. Five micrograms of YefMSa1, YoeBSa1-Y88F, YoeBSa1-Y88TAG, or YoeBSa1-Y88ONBY was precipitated according to a previously published method.26 YoeBSa1Y88ONBY was exposed to 312 nm light on a UV transilluminator for 0−600 s prior to precipitation. Precipitated, airdried protein was analyzed by electrospray ionization mass spectrometry (ESI-MS) at the University of Illinois Mass Spectrometry Laboratory. Agarose Gel RNase Activity Assay. pET-28a-yef MyoeBSa1 was digested with XhoI (NEB) at 37 °C for 3 h. The fully linearized plasmid was extracted once with a 24.5:24.5:1 phenol/chloroform/isoamyl alcohol mixture and twice with chloroform, precipitated with 3 M NaOAc (pH 5.3) and 100% EtOH, and resuspended in nuclease-free water. One microgram of linearized plasmid was used as the template for standard RNA synthesis with the T7 High Yield RNA Synthesis Kit (NEB) according to the manufacturer’s instructions. RNA was purified with reagents from Total RNA Kit I (Omega Bio-Tek) according to the RNA Cleanup protocol from the RNeasy Mini Handbook (Qiagen). RNase assays were performed according to a modified published method.19 For the light dependence of decaging, 10 pmol of YoeBSa1-Y88ONBY in 50 mM Tris and 5% glycerol (pH 8.0) was exposed to UV light for 0−5 min, followed by the addition of 320 ng of yef M-yoeBSa1 RNA with Human Placental RNase Inhibitor (NEB) at a final concentration of 1 unit/μL. Reactions were incubated at 37 °C for 2 h and quenched by addition of 1 μg of proteinase K (Invitrogen) and incubation at 37 °C for 15 min. Eleven microliters of RNA loading dye I (95% formamide, 18 mM EDTA, 0.025% SDS, and 0.025% bromophenol blue) was then added, and samples were incubated at 95 °C for 5 min immediately prior to electrophoresis on 1.2% agarose, 0.5× TBE [45 mM Tris-borate and 1 mM EDTA (pH 8.3)], 0.1 μg/ mL ethidium bromide gels. For the inhibition of YoeBSa1 by YefMSa1, YoeBSa1 (10, 20, or 30 pmol) in 50 mM Tris and 5% glycerol (pH 8.0) was exposed to UV light for 3 min. YefMSa1 (0, 10, 20, or 30 pmol) was then added. Following incubation at 37 °C for 30 min to allow formation of the YefMYoeBSa1complex, 320 ng of yef M-yoeBSa1 RNA was added with Human Placental RNase Inhibitor at a final concentration of 1 unit/μL. Reactions were incubated at 37 °C for 1 h, quenched, and analyzed as described above. For the time course of YoeBSa1 and YefMSa1 RNase activity, 10 pmol of YoeBSa1Y88ONBY, YoeBSa1-Y88F, YoeBSa1-Y88TAG, or YefMSa1 was incubated with 320 ng of yef M-yoeBSa1 RNA in the presence of 1 unit/μL Human Placental RNase Inhibitor in 50 mM Tris and 5% glycerol (pH 8.0). One set of reactions containing YoeBSa1-Y88ONBY was exposed to UV light for 3 min prior to the addition of RNA. Reactions were incubated at 37 °C for 1− 20 h, quenched, and analyzed as described above. Polyacrylamide Gel RNase Activity Assay. Quikchange site-directed mutagenesis was performed with primers PP1QC1-F and PP1QC1-R to insert a G into Pentaprobe 1 and with primers PP1QC2-F and PP1QC2-R, PP2QC-F and PP2QC-R, PP4QC-F and PP4QC-R, PP6QC-F and PP6QC-R, PP7QC-F and PP7QC-R, PP8QC-F and PP8QC-R, PP9QC-F and PP9QC-R, PP10QC-F and PP10QC-R, and PP12QC-F and PP12QC-R (Table S1 of the Supporting Information) to introduce XbaI sites into Pentaprobes 1, 2, 4, 6−10, and 12, respectively. Site-directed mutagenesis was carried out with the Quikchange site-directed mutagenesis kit (Stratagene) according to the manufacturer’s instructions, with the modification that E. coli DH5α was used as the host strain. Pentaprobe

reached 0.4−0.6. Protein expression was induced with 1 mM IPTG at 37 °C with shaking at 250 rpm for 4 h. The culture was harvested by centrifugation at 6000g for 5 min at 4 °C. Cell pellets were frozen at −20 °C, thawed on ice for 30 min, and resuspended in 10 mL of cold lysis buffer [20 mM Tris, 500 mM NaCl, and 60 mM imidazole (pH 7.9)]. Cells were lysed by sonication on ice at 40% amplitude for 5 min with a 1 s pulse. The lysate was cleared by centrifugation at 35000g for 30 min at 4 °C. The supernatant was batch-loaded onto 1 mL of 1:1 Ni-NTA agarose (Qiagen) at 4 °C for 30 min with inversion. The resin was washed with 20 mL of cold lysis buffer and eluted with 10 mL of cold elution buffer A [50 mM Tris, 500 mM NaCl, 500 mM imidazole, 1 mM TCEP, and 10% glycerol (pH 7.9)]. The eluted fraction was concentrated to ∼0.5 mL using an Ultra-15 Centrifugal Filter Unit with an Ultracel-3 membrane (Amicon), 0.2 μm filtered, and further purified on a HiLoad 16/60 Superdex 75 PG column (GE Healthcare) using fast performance liquid chromatography (FPLC) buffer A [50 mM Tris, 200 mM NaCl, 1 mM TCEP, and 10% glycerol (pH 7.9)]. Fractions containing pure protein were pooled and concentrated to ∼0.5−1 mL. Purity was assessed by sodium dodecyl sulfate−polyacrylamide gel electrophoresis (SDS−PAGE) using 4−20% TGX Mini-PROTEAN gels (Bio-Rad). The concentration was determined by densitometry and by the bicinchoninic acid (BCA) assay (Pierce) performed according to the manufacturer’s instructions, with the modification that lysozyme standards were used instead of bovine serum albumin (BSA) standards. Purification of YoeBSa1-Y88ONBY. pET-28a-yoeBSa1Y88TAG and pEVOL-ONBY were introduced into E. coli NiCo21(DE3). A single colony from a freshly streaked plate was inoculated into LB medium supplemented with kanamycin and chloramphenicol and grown at 37 °C with shaking at 250 rpm overnight (14−16 h). The overnight culture was diluted 1:100, 100 mM ONBY dissolved in 1 M NaOH was added to a final concentration of 1 mM, and the culture was grown at 37 °C with shaking at 250 rpm in the dark. When the A600 of the culture reached 0.5−0.6, arabinose was added to a final concentration of 0.2% to induce expression of ONBY-aaRS. When the A600 of the culture reached 1.0−1.2, IPTG was added to a final concentration of 1 mM to induce expression of YoeBSa1-Y88ONBY. Expression was allowed to proceed at 37 °C for 15 h. The culture was harvested, and YoeBSa1-Y88ONBY was purified in the dark as described above for YoeBSa1-Y88F and YoeBSa1-Y88TAG. Purification of YefMSa1. pET-28a-yef MSa1 was introduced into E. coli NiCo21(DE3), and protein expression and purification were performed as described for YoeBSa1-Y88F and YoeBSa1-Y88TAG, with the modification that YefMSa1 was eluted with 10 mL of cold elution buffer B [20 mM Tris, 500 mM NaCl, and 500 mM imidazole (pH 7.9)]. Gel filtration was performed twice using FPLC buffer B [20 mM Tris and 500 mM NaCl (pH 7.9)] to remove RNase contamination. Fractions corresponding to the second major peak from the first gel filtration step were pooled, concentrated, and subjected to a second gel filtration step. Fractions corresponding to the second major peak from the second gel filtration step were pooled, concentrated, and used in experiments. Purity was assessed by SDS−PAGE using 4−20% TGX Mini-PROTEAN gels (Bio-Rad). Protein concentration was determined by the BCA assay (Pierce) performed according to the manufacturer’s instructions using BSA standards. 190

dx.doi.org/10.1021/bi4008098 | Biochemistry 2014, 53, 188−201

Biochemistry

Article

plasmids were digested with XbaI (NEB) at 37 °C for 3 h. Fully linearized plasmids were purified by phenol/chloroform extraction as described above. RNA was synthesized and purified as described above. RNase assays were performed according to a modified published method.27 One microgram of YoeBSa1-Y88ONBY was incubated with 1 μg of Pentaprobe RNA in 50 mM Tris (pH 8.0) for 0.5−2 h at 37 °C. Reactions were quenched by addition of 1 μg of proteinase K and incubation at 37 °C for 15 min. An equal volume of RNA loading dye II (95% formamide, 5 mM EDTA, and 0.025% bromophenol blue) was then added, and the reactions were incubated at 95 °C for 5 min to denature the RNA. The products were visualized by electrophoresis on 8% polyacrylamide TBE−urea gels [89 mM Tris-borate, 2 mM EDTA, and 8 M urea (pH 8.3)] poststained with ethidium bromide. Matrix-Assisted Laser Desorption Ionization (MALDI) RNase Activity Assay. PP7-1, PP7-2, and PP7-3 were synthesized by Genscript. Ten micrograms of YoeBSa1Y88ONBY was incubated with 2 μg of oligonucleotide for 1 or 2 h at 37 °C. Reactions were quenched by addition of 10 μg of proteinase K (Invitrogen) and incubation at 37 °C for 30 min followed by precipitation with 5 M NH4OAc (final concentration of 2 M) and 3 volumes of 100% EtOH at −80 °C. Pellets were washed with ice-cold 70% EtOH, resuspended in 1 μL of H2O, and analyzed by matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) at the University of Illinois Mass Spectrometry Laboratory. High-Performance Liquid Chromatography (HPLC) RNase Activity Assay. The fluorogenic chimeric oligonucleotide substrate 5′-6-FAM-AACrArArArArGrArArAAATTIABkFQ-3′ (6-FAM, 6-carboxyfluorescein fluorophore; IABkFQ, Iowa Black fluorophore quencher) and cleavage products 5′-6-FAM-AACrArArArArG-3′ and 5′-rArArAAATTIABkFQ-3′ were synthesized by IDT. YoeBSa1 (20 μM) was incubated with oligonucleotide (30 μM) in buffer at 25 °C for 5 h. HPLC was performed using an Alliance HPLC System (e2695 Separations Module, Waters) with detection at 260 nm (2489 UV/visible Detector, Waters). The full-length oligonucleotide was separated from the cleavage products on a YMCbasic S5 column (4.6 mm × 150 mm, 5 μm, Waters) using a linear gradient from 100 mM triethylammonium acetate (TEAA) (pH 7.0) to a mixture of 50 mM TEAA and 50% acetonitrile (pH 7.0) over 25 min. Peak fractions were collected, concentrated to 5−10 μL, and analyzed by MALDI-MS at the University of Illinois Mass Spectrometry Laboratory. Fluorometric Assay. Wells of a black 384-well plate were filled with 15 μL of 0.5−20 μM intact fluorogenic substrate or cleavage products diluted in assay buffer [200 mM sodium phosphate (pH 6.0) and 5% glycerol] and allowed to equilibrate for 30 min at room temperature. YoeBSa1Y88ONBY was diluted to 10 μM in assay buffer, exposed to UV light at 312 nm for 3 min, and added to wells containing intact substrate or cleavage products to a final concentration of 5 μM. Fluorescence was measured once every minute for 100 min using a Criterion Analyst AD instrument (Molecular Devices) with 485 ± 15 nm excitation and 530 ± 15 nm emission filters and a 505 nm cutoff dichroic mirror. The fluorophore was excited with a 1000 W continuous xenon arc lamp with 10 reads per well. Three separately purified batches of YoeBSa1-Y88ONBY were each assayed in technical triplicate on two different days. Results are the average of the average rate for each batch of protein.

Calibration Plot. Fluorescence values for 1:1 molar mixtures of the cleavage products at 30 min after addition of YoeBSa1 were used to construct a calibration plot of picomoles of cleaved substrate versus relative fluorescence units (RFU). A separate calibration plot was constructed each time the fluorometric assay was performed. Kinetic Analysis. In some of the progress curves, an increase in fluorescence was not observed until ∼15 min after the addition of YoeBSa1. However, the increase in measured fluorescence was linear over the majority of the remainder of the assay. Consequently, initial rates were calculated from the linear portion of the progress curves between 20 and 30 min. Fluorescence values were corrected by subtracting the fluorescence measured at 20 min from all subsequent time points. Corrected fluorescence values were converted to picomoles of cleaved substrate using the slope from the calibration plot, and linear regression was performed using Microsoft Excel to obtain initial velocities. Linear velocities were plotted versus substrate concentration, and the resulting data points were fit with the Hill equation using OriginPro version 8.0.

■

RESULTS Prevalence, Conservation, and Transcription of yef MyoeBSa1 and yef M-yoeBSa2 in MRSA Clinical Isolates. The artificial activation of TA systems is of significant interest as an intriguing antibacterial strategy.11−14 YoeBSa1 and YoeBSa2 specifically present outstanding targets for this approach, as expression of YoeBSa1 and YoeBSa2 in the absence of their respective antitoxins, YefMSa1 and YefMSa2, induces growth arrest in E. coli.28 For artificial activation of YoeBSa1 or YoeBSa2 to be an effective antibacterial strategy, YefM-YoeBSa1 and YefM-YoeBSa2 must be present and functional in clinical isolates of S. aureus. Thus, the presence, conservation, and transcription of yef M-yoeBSa1 and yef M-yoeBSa2 were investigated in a collection of 78 clinical isolates of MRSA from three Illinois hospitals and the Network on Antimicrobial Resistance in S. aureus (NARSA). Multiple-locus variable number of tandem repeats analysis previously confirmed that these isolates were not clonal.21 The total DNA of these isolates was probed for the presence of yef M-yoeBSa1 and yef M-yoeBSa2 using PCR with intragenic specific primers (Figure 1A). The yef M-yoeBSa1 and yef MyoeBSa2 genes were present in 99% (77 of 78) of the clinical isolates (Table S2 of the Supporting Information). Approximately 10% of the PCR products were subjected to DNA sequencing, and the sequences were aligned with the reference genome from the S. aureus COL strain using CLUSTAL W23 (Figures S1 and S2 of the Supporting Information) and compared with yef M-yoeBSa1 and yef M-yoeBSa2 loci from published S. aureus genomes using BLAST.24 The yef M-yoeBSa1 PCR products were >97% identical with the yef M-yoeBSa1 genes in 29 of the 30 genomes containing that locus, while the yef MyoeBSa2 PCR products were at least 96% identical with the yef M-yoeBSa2 genes in all 26 genomes containing that locus. PCR products of ∼1.3 and ∼2.5 kb resulted from attempts to detect yef M-yoeBSa1 and yef M-yoeBSa2, respectively, in NRS27. DNA sequence analysis revealed that the product amplified by yef M-yoeBSa1-specific primers spanned a phage transcriptional repressor and a DNA polymerase III α subunit, while the product amplified by yef M-yoeBSa2-specific primers spanned an ornithine cyclodeaminase, a siderophore biosynthesis protein, and a multidrug resistance efflux pump. Sites of partial 191

dx.doi.org/10.1021/bi4008098 | Biochemistry 2014, 53, 188−201

Biochemistry

Article

biology techniques than yef M-yoeBSa2, a number of strategies were explored in efforts to obtain pure, functional YoeBSa1. The most common method employed to obtain a functional TA system toxin for in vitro characterization involves coexpression of the antitoxin with the toxin, purification of the resulting TA complex, isolation of the toxin by denaturation of the complex, and subsequent refolding. Active YoeBEc has been obtained by dissociation from YefMEc in 6 M guanidine hydrochloride (GuHCl) followed by refolding via gradual dialysis into HEPES buffer.19 YoeBEc and YoeBSa1 share a high degree of sequence homology, suggesting that a similar method could allow purification of functional YoeBSa1. The yef MyoeBSa1 operon was therefore cloned into pET-28a with a hexahistidine tag at the N-terminus of YefMSa1 to facilitate purification, and the complex was expressed in E. coli and purified using Ni-NTA resin. A variety of conditions were screened to identify an optimal method for denaturing, purifying, and refolding YoeBSa1. In each case, the YefMYoeBSa1 complex was denatured by extended dialysis against either 6 M GuHCl or 8 M urea, YefMSa1 was extracted with NiNTA resin, and the presence and purity of the remaining YoeBSa1 were assessed using SDS−PAGE. If 6 M GuHCl was used as the denaturant, the recaptured YefMSa1 was highly pure, but YoeBSa1 was not recovered in the unbound fraction, probably because of the low initial ratio of YoeBSa1 to YefMSa1 and the necessity of diluting and precipitating samples containing GuHCl for SDS−PAGE. In contrast, when 8 M urea was used as the denaturant, YoeBSa1 was recovered, but a significant amount of residual YefMSa1 was also present. Efforts to refold the impure toxin by dilution or gradual dialysis resulted in substantial precipitation. These unpromising results led to the abandonment of denaturing purification and refolding as a viable approach to obtaining large quantities of pure, active YoeBSa1. An alternative to denaturing purification of the toxin from the TA complex is to use a commercially available protease to selectively degrade the labile antitoxin from the TA complex, leaving the toxin unscathed.27 The YefM-YoeBSa1 complex was expressed and purified as described above and subjected to digestion with trypsin. Analysis of the digest products by SDS− PAGE suggested that YoeBSa1 remained intact while YefMSa1 was rapidly and selectively degraded. However, the YoeBSa1 protein obtained from trypsin digestion of YefM-YoeBSa1 did not bind to YefMSa1 in pull-down experiments. Native PAGE of the digestion time course suggested that a fragment of YefMSa1 remained bound to YoeBSa1, prohibiting complex formation and indicating that this approach could not be used to obtain pure YoeBSa1. The yoeBSa1 gene was then cloned at the C-terminus of glutathione S-transferase (GST) in hopes that a larger fusion partner would reduce the toxicity of YoeBSa1 by preventing it from binding to the ribosome. However, all sequenced clones contained frameshift mutations introducing premature stop codons in the yoeBSa1 gene. Two rounds of site-directed mutagenesis were performed to correct these mutations. Additional premature stop codons or inactivating mutations were introduced in each round, suggesting that low levels of full-length GST-YoeBSa1, produced by leaky expression from the T7 promoter even in the absence of T7 RNA polymerase, retained the ability to bind to the ribosome, inhibit translation, induce growth arrest, and prevent colony formation. Only mutant clones encoding premature stop codons were not toxic. These results hinted that the C-terminal region of YoeBSa1 is

Figure 1. yef M-yoeBSa1 and yef M-yoeBSa2 are prevalent and transcribed in MRSA clinical isolates. (A) Locations of homology for primers used in PCR and RT-PCR. Primer sequences were designed from the S. aureus COL genome. (B) RT-PCR analysis of yef M-yoeBSa1 (Sa1, top two panels) and yef M-yoeBSa2 (Sa2, bottom two panels) transcription in MRSA clinical isolates. Lane M contains a DNA ladder [1517, 1200, 1000, 900, 800, 700, 600, 500, 400, 300, 200, and 100 bp (NEB)]. Plus and minus signs denote the inclusion and exclusion, respectively, of reverse transcriptase. Clinical isolates are identified by strain number.

complementarity were identified between the yef M-yoeBSa1- and yef M-yoeBSa2-specific primers and these genes, which could allow amplification in the absence of yef M-yoeBSa1 and yef MyoeBSa2. To confirm the absence of yef M-yoeBSa1 and yef MyoeBSa2 in NRS27, the yef MSa1, yoeBSa1, yef M-yoeBSa1, yef MSa2, yoeBSa2, and yef M-yoeBSa2 operons were individually amplified using primers designed to clone each of the full genes. PCR products were detected in the positive control strain NRS76, but not in NRS27. These results indicate that the yef M-yoeBSa1 and yef M-yoeBSa2 genes are not present in NRS27. To investigate the transcription of yef M-yoeBSa1 and yef MyoeBSa2 in MRSA, RT-PCR was performed on total RNA from eight isolates using the same primers used in the PCR screen. yef M-yoeBSa1 and yef M-yoeBSa2 were transcribed as bicistronic messages in each of the strains (Figure 1B). No PCR products were detected in the absence of reverse transcriptase, indicating the absence of DNA contamination. Taken together, these results suggest that yef M-yoeBSa1 and yef M-yoeBSa2 are widespread, conserved, and transcribed in clinical MRSA isolates. Thus, an activator of YoeBSa1 or YoeBSa2 with antibacterial activity could have broad efficacy against S. aureus. Photocaging Allows Expression of YoeBSa1 in E. coli. YoeBEc exhibits ribosome-dependent RNase activity in vitro and in E. coli.20 YoeBSa1 and YoeBSa2 were found to exhibit RNase activity similar to that of YoeBEc upon overexpression in E. coli, suggesting that they are ribosome-dependent RNases with the same mechanism of action as YoeBEc.28 Intriguingly, YoeBEc also possesses “residual” ribosome-independent RNase activity.19 Evaluation of the possibility that YoeBSa1 and YoeBSa2 might also possess such activity necessitates the expression and purification of full-length, functional YoeBSa1 and YoeBSa2. However, YoeBSa1 and YoeBSa2 inhibit translation initiation and induce growth arrest in E. coli,28 effectively preventing overexpression and characterization. As yef M-yoeBSa1 proved to be more amenable to manipulation using standard molecular 192

dx.doi.org/10.1021/bi4008098 | Biochemistry 2014, 53, 188−201

Biochemistry

Article

Figure 2. ESI-MS analysis of YoeBSa1 mutants. (A) YoeBSa1-Y88TAG (calculated molecular mass of 12307 Da and observed molecular mass of 12303 Da). (B) YoeBSa1-Y88F (calculated molecular mass of 12454 Da and observed molecular mass of 12450 Da). (A and B) Gel inset lanes: Kaleidoscope prestained standards (Bio-Rad), expression culture lysate immediately prior to induction with IPTG, and expression culture lysate 4 h postinduction (from left to right, respectively). The asterisk indicates the band corresponding to YoeBSa1-Y88TAG in panel A and YoeBSa1-Y88F in panel B. (C) YoeBSa1-Y88ONBY prior to exposure to UV light (calculated molecular mass of 12606 Da and observed molecular mass of 12574 Da). (D−H) YoeBSa1-Y88ONBY exposed to UV light for 1, 2, 3, 4, and 5 min, respectively (calculated molecular mass of 12470 Da and observed molecular mass of 12468−12469 Da).

activity and toxicity in E. coli,19 suggesting that similar mutations to the homologous C-terminal Y88 of YoeBSa1 might sufficiently reduce toxicity to allow expression in E. coli. To investigate the contribution of Y88 to the toxicity of YoeBSa1, the TAT codon for Y88 in YoeBSa1 was changed to TAG for the amber stop codon (Y88TAG) or to TTT for phenylalanine (Y88F). The genes encoding these mutants were

necessary for activity and toxicity. As the C-terminal residues H83 and Y84 of YoeBEc are required for both in vitro RNase activity and toxicity in E. coli,19 the inability to clone the fulllength yoeBSa1 gene at the C-terminus of GST suggested that the analogous H87 and Y88 in YoeBSa1 have similar roles. Mutation of the C-terminal Y84 of YoeBEc to phenylalanine or alanine was previously found to diminish both in vitro RNase 193

dx.doi.org/10.1021/bi4008098 | Biochemistry 2014, 53, 188−201

Biochemistry

Article

Decaged YoeBSa1 Is a Ribosome-Independent RNase. The ribosome-independent RNase activity of YoeBSa1 was assessed with respect to yef M-yoeBSa1 RNA in vitro. Decaging of YoeBSa1-Y88ONBY resulted in UV light-dependent degradation of the RNA (Figure 3A). In agreement with ESI-MS data

cloned into pET-28a and expressed in E. coli. The resulting proteins were purified with yields of 5 mg of YoeBSa1-Y88TAG and 2.5 mg of YoeBSa1-Y88F per liter of culture. ESI mass spectrometry (ESI-MS) showed that the molecular masses of these mutants matched the predicted values [YoeBSa1-Y88TAG, expected molecular mass of 12307 Da and observed molecular mass of 12303 Da (Figure 2A); YoeBSa1-Y88F, expected molecular mass of 12454 Da and observed molecular mass of 12450 Da (Figure 2B)]. These results indicated that Y88 contributes to YoeBSa1 toxicity in E. coli and suggested that a nonpermanent modification of the structure of Y88 might sufficiently alleviate the toxicity of YoeBSa1 to allow expression of the full-length protein in E. coli. Unnatural amino acid (UAA) mutagenesis allows the incorporation of a noncanonical amino acid site-specifically into a protein via the use of an aminoacyl-tRNA synthetase (aaRS)/tRNA pair that is orthogonal to the host organism’s translational machinery.29−31 The photocaged UAA o-nitrobenzyl tyrosine (ONBY) has been incorporated into a number of proteins in which a tyrosine is critical for enzymatic activity.32−36 Mutation of tyrosine to ONBY “cages” the enzyme by inhibiting catalysis, substrate binding, or both. Irradiation with UV light between 300 and 365 nm releases the photocaging o-nitrobenzyl group,37 revealing the free tyrosine and activating the enzyme for catalysis. As Y88 contributes to the toxicity and, presumably, the activity of YoeBSa1, it was hypothesized that mutation of Y88 to ONBY would allow expression of an inactive, nontoxic YoeBSa1 variant that could be activated by UV light following expression and purification. The pEVOL plasmids for UAA mutagenesis encode an optimized amber (TAG) stop codon suppressor tRNA and two copies of an evolved UAA-specific Methanocaldococcus jannaschii aaRS, one under the control of a constitutive glnS′ promoter and the other under the control of an arabinoseinducible araBAD promoter, which allows the expression level of the aaRS to be finely tuned.38 As Y88 is the last residue in YoeBSa1, it would be challenging to purify ONBY-containing YoeBSa1 from prematurely truncated YoeBSa1. A variety of expression conditions were therefore screened by ESI-MS for maximal incorporation of ONBY into YoeBSa1. Maximal incorporation was achieved when 1 mM ONBY was present in the culture medium from the beginning of the expression, when aaRS expression was induced in early logarithmic growth phase, and when YoeBSa1 expression was induced in late logarithmic or early stationary phase and allowed to proceed overnight at 37 °C. Using this method, 1 mg of pure YoeBSa1Y88ONBY was obtained per liter of culture. ESI-MS revealed that the mass of the full-length caged protein was ∼30 Da lower than predicted [YoeBSa1-Y88ONBY, expected molecular mass of 12606 Da and observed molecular mass of 12574 Da (Figure 2C)]. This discrepancy is attributed to reduction of the nitro group of ONBY to an amino group, a phenomenon that has been observed when ESI-MS is performed in protic solvents, resulting in a loss of 30 Da that corresponds to the observed mass shift.39 Importantly, very little truncated YoeBSa1-Y88TAG was present (expected molecular mass of 12307 Da and observed molecular mass of 12305 Da). UV light-induced loss of the o-nitrobenzyl moiety was followed by ESI-MS [YoeBSa1Y88, expected molecular mass of 12470 (Figure 2D−H)]. The extent of decaging increased as the extent of UV exposure was increased up to 3 min, after which no further decaging was observed (Figure 2F−H).

Figure 3. RNase activity of YoeBSa1 mutants. (A) RNase activity of YoeBSa1-Y88ONBY exposed to UV light for 0, 5, 10, 20, 30, 60, 120, 180, 240, or 300 s and incubated with yef M-yoeBSa1 RNA for 2 h. Buffer controls were incubated with yef M-yoeBSa1 RNA for 0 or 2 h. (B) Inhibition of YoeBSa1 by YefMSa1. YoeBSa1-Y88ONBY was exposed to UV light for 3 min. YefMSa1 and YoeBSa1 were mixed and incubated at 37 °C for 30 min to allow formation of the YefM-YoeBSa1 complex prior to incubation with yef M-yoeBSa1 RNA at 37 °C for 1 h. A minus sign designates 0 pmol of protein, a plus sign designates 10 pmol of protein, and right triangles designate increasing amounts of protein from 10 to 30 pmol. (C) RNase activity of YoeBSa1, YoeBSa1Y88ONBY, YoeBSa1-Y88F, YoeBSa1-Y88TAG, and YefMSa1. Ten picomoles of protein was incubated with yef M-yoeBSa1 RNA for 0, 1, 2, 4, 8, 12, 16, or 20 h. Lane M contains an ssRNA ladder [1000, 500, 300, 150, 80, and 50 nucleotides (NEB)]. Lane B contains buffer and RNA at 20 h. In the top panel only, YoeBSa1-Y88ONBY was exposed to UV light for 3 min.

showing that the extent of decaging did not increase with additional UV exposure after 3 min (Figure 2F), the RNase activity of YoeBSa1-Y88ONBY also did not increase with additional UV exposure after 3 min (Figure 3A). YoeBSa1 activity was inhibited by the addition of an equimolar amount of YefMSa1 (Figure 3B), demonstrating that the observed RNase activity was due specifically to YoeBSa1 and not to RNase 194

dx.doi.org/10.1021/bi4008098 | Biochemistry 2014, 53, 188−201

Biochemistry

Article

Figure 4. YoeBSa1 cleaves RNA at guanosine residues. (A) RNase activity of YoeBSa1 toward Pentaprobes 1, 4, 7, and 10. Lane M contains an ssRNA ladder [1000, 500, 300, 150, 80, and 50 nucleotides (NEB)]. In the buffer lanes, RNA was incubated in buffer alone for 0 or 2 h. In the −UV lanes, YoeBSa1-Y88ONBY was incubated with RNA for 2 h. In the +UV lanes, YoeBSa1-Y88ONBY was exposed to UV light for 2 min and incubated with RNA for 0.5, 1, 1.5, or 2 h. (B) Primary sequences of Pentaprobe 7 and Pentaprobe 7 oligonucleotides PP7-1, PP7-2, and PP7-3. YoeBSa1 cleavage sites identified by MALDI-MS are denoted with arrows. (C) YoeBSa1 consensus cleavage sequence calculated by WebLogo.74

YoeBEc, which cleaves RNA after purine residues with a preference for adenosine.19 To identify the specific sequence recognized and cleaved by YoeBSa1 within Pentaprobe 7, cleavage of three overlapping oligonucleotides spanning Pentaprobe 7 (Figure 4B) was assessed by MALDI-MS. YoeBSa1 cleaved each oligonucleotide selectively after guanosine, leaving a 3′-cyclic phosphate on the 5′-RNA product. This suggests that YoeBSa1 is a guanosinespecific RNase in vitro and furthermore that the mechanism of YoeBSa1 RNA cleavage involves activation of the 2′-OH for nucleophilic attack of the 3′-phosphodiester bond. Fragments corresponding to both the 5′- and 3′-products were observed for 5 of the 9 guanosines in PP7-1, 6 of 13 in PP7-2, and 1 of 4 in PP7-3. Most of the noncleaved guanosines were near the termini of the oligonucleotides, which reduces the likelihood of observing cleavage at these sites by MALDI because of the 2 kDa lower mass limit of the detector and a reduction in MALDI sensitivity with an increase in oligonucleotide length. YoeBSa1 may also require a minimum number of residues 5′ or 3′ from the cleavage site to bind and cleave RNA and thus may skip guanosines near the termini of an oligonucleotide. In the consensus sequence cleaved by YoeBSa1, adenosine residues precede and follow the guanosine at the cleavage site (Figure 4C). This may be an artifact of oligonucleotide design and selection, as most of the guanosines in Pentaprobe 7 are preceded by one or more adenosines. However, it is also possible that YoeBSa1 prefers to cleave after guanosines in the midst of purine-rich sequences. The fact that YoeBSa1 cleaved

contamination. This result also suggests that YefMSa1 inhibits YoeBSa1 at a 1:1 ratio, which is identical to the ratio of YefMEc to YoeBEc required to inhibit YoeBEc in a similar in vitro assay.19 Comparison of the activity of decaged YoeBSa1 with that of YoeBSa1 mutants and YefMSa1 reveals that YoeBSa1-Y88ONBY retains weak in vitro RNase activity, YoeBSa1-Y88F degrades RNA very slowly, and no detectable RNase activity is observed for YoeBSa1-Y88TAG or YefMSa1 (Figure 3C). YoeBSa1 Cleaves RNA after Guanosine Residues. The Pentaprobes are a set of 12 plasmids that together encode every possible combination of five nucleotides in sequences of ∼100 nucleotides per plasmid.40 The Pentaprobes have been used to determine the sequence specificity of RNases with recognition sequences of five or fewer nucleotides. Cleavage of each Pentaprobe by the RNase of interest is assessed by PAGE. Once cleaved Pentaprobes are identified, deconvolution occurs via MALDI-MS analysis of cleavage of small oligonucleotides.27 The RNase activity of YoeBSa1 toward each of the 12 Pentaprobe RNA transcripts was assessed by denaturing PAGE. YoeBSa1 was least active toward Pentaprobe 1 and most active toward Pentaprobes 4, 7, and 10 (Figure 4A; other Pentaprobes not shown). Cleavage of Pentaprobe 7 was the most dramatic, with rapid and significant degradation of the full-length parent band and the appearance of a number of smaller discrete product bands, indicating that YoeBSa1 cleaves this Pentaprobe at multiple sites. The sequence of Pentaprobe 7 is rich in purine residues (Figure 4B), suggesting that the sequence specificity of YoeBSa1 might be similar to that of 195

dx.doi.org/10.1021/bi4008098 | Biochemistry 2014, 53, 188−201

Biochemistry

Article

Figure 5. Kinetic analysis of YoeBSa1 using the fluorometric assay. (A) Fluorogenic substrate design. “r” designates RNA nucleotides. (B) HPLC traces of products of YoeBSa1 activity: black for 30 μM intact substrate, green for 30 μM 5′-cleavage product, cyan for 30 μM 3′-cleavage product, and blue for 30 μM substrate cleaved by 20 μM YoeBSa1 after 5 h at 25 °C. Peak fractions from the blue trace were analyzed by MALDI-MS and are labeled with the observed molecular masses of the 5′- and 3′-cleavage products (calculated molecular masses of 3115.0 Da and 2602.8 Da, respectively). (C) Representative set of progress curves from one experiment. (D) Initial slopes of fluorometric assay curves (●) with a Hill fit (). Error bars represent the standard deviation (n = 3 separately purified batches of YoeBSa1, each assayed in technical triplicate on two different days; plotted data are the average of the average for each batch).

standards (Figure 5B), suggesting that cleavage occurred primarily at guanosine, as predicted. MALDI-MS analysis of fractions collected from the elution peaks confirmed that the majority of cleavage events occurred at guanosine (Figure S3 of the Supporting Information). These results corroborate the guanosine specificity of YoeBSa1 ribosome-independent RNase activity.19 To determine the kinetic parameters of YoeBSa1 as a baseline for future high-throughput screening efforts, the RNase activity of YoeBSa1 toward the fluorogenic substrate was assessed in 384-well plate format. YoeBSa1 (5 μM) was incubated with a range of concentrations of the fluorogenic substrate (0.5−20 μM) to produce a set of progress curves (representative data from one replicate of one experiment shown in Figure 5C). For each experiment, a calibration curve was constructed by mixing the two chimeric products resulting from YoeBSa1 cleavage at a 1:1 molar ratio in the presence of YoeBSa1 (5 μM). The relationship between the measured fluorescence and the concentration of the cleavage products was linear up to 1.5 μM. This calibration curve was used to convert relative fluorescence units (RFU) at 530 nm to picomoles of cleaved substrate. Ideally, initial rates would be measured immediately following addition of YoeBSa1 to the substrate. However, in some experiments, a significant increase in fluorescence was not observed until ∼15 min after the addition of YoeBSa1. Consequently, the rates plotted in Figure 5D were determined from the linear portion of the progress curves between 20 and 30 min.

PP7-3 at only one of the three internal guanosines suggests that the ability of YoeBSa1 to cleave free mRNA may be inhibited by secondary structure, as PP7-3 had more predicted secondary structure than PP7-1 and PP7-2, which may have limited the ability of YoeBSa1 to access other potential cleavage sites in PP7-3. Kinetic Characterization of YoeBSa1 RNase Activity. With the objective of developing a YoeBSa1 substrate that could be used to assess the activation of this RNase in a highthroughput setting, a fluorogenic oligonucleotide substrate was designed based on the data presented in Figure 4. An analogous design was previously used for the creation of a substrate for the ribosome-independent RNase MazF.41,42 One of the sequences from PP7 that was cleaved by YoeBSa1 was converted into a 15-mer chimeric oligonucleotide with eight internal RNA residues surrounded by DNA nucleotides for stability (Figure 5A). Cleavage of this substrate was predicted to occur after the central guanosine residue. A 6-carboxyfluorescein fluorophore (excitation at 495 nm and emission at 520 nm) and an Iowa Black FQ quencher (absorbance maximum at 530 nm) were appended to the 5′- and 3′-ends, respectively, of the oligonucleotide. In the intact substrate, proximity allows the quencher to absorb the fluorescence emitted by the fluorophore. Cleavage of the substrate increases the distance between the fluorophore and the quencher, producing an increase in fluorescence that can be monitored spectrophotometrically. The ability of YoeBSa1 to cleave this substrate was assessed by HPLC. The retention times of the products from YoeBSa1 activity overlapped with those of the independently synthesized 196

dx.doi.org/10.1021/bi4008098 | Biochemistry 2014, 53, 188−201

Biochemistry

Article

Information). As a result, the activity measured in the fluorometric assay is the sum of the rates at which YoeBSa1 cleaves after all of the RNA residues in the substrate. The preference for guanosine over adenosine suggests that cleavage after guanosine is faster than cleavage after adenosine. Thus, at nonsaturating substrate concentrations, the observed rate will be influenced primarily by cleavage after guanosine. As the substrate concentration increases, the proportion of cleavage events that are catalyzed after adenosine rather than guanosine will also increase. Eventually, at supersaturating substrate concentrations, the proportion of cleavage events at adenosine will increase to the degree that it will cause a measurable decrease in the overall rate, as observed in Figure 5D. Consequently, Vmax for guanosine-specific substrate cleavage cannot be determined from the kinetic data. However, assuming that cleavage after adenosine makes a limited contribution to the measured rate at low substrate concentrations, fitting the kinetic data at substrate concentrations below those at which a measurable decrease in rate occurs will allow extrapolation to an estimate for Vmax. As it is possible that cleavage after adenosine makes a non-negligible contribution to the overall rate even at low substrate concentrations, this approach will provide minimal estimates only for Vmax and Km. The Hill equation (eq 3) was originally derived to describe the cooperative binding of ligands to a protein containing multiple binding sites when one or more ligands are already bound:

Traditional Michaelis−Menten enzyme kinetics are characterized by a hyperbolic rate, V, versus substrate concentration, [S], curve that can be fit by the equation V=

Vmax[S] K m + [S]

(1)

where Vmax is the maximal reaction velocity and Km is the Michaelis constant, equal to the substrate concentration at which half-maximal activity is observed. This equation describes a hyperbolic rate that increases linearly when [S] is low and asymptotically approaches Vmax at high values of [S].43,44 The rate data in Figure 5D reveal that the kinetics of YoeBSa1 RNase activity toward the fluorogenic substrate are complex, with a sigmoidal increase in rate up to 10 μM substrate, followed by a marked decrease in rate at 15 and 20 μM substrate. The shape of the rate data suggests that the activity of YoeBSa1 is influenced by positive cooperativity at low substrate concentrations and by substrate inhibition at high substrate concentrations. However, careful consideration of the assay conditions and the nature of the fluorogenic substrate points to alternative explanations for the apparent cooperativity and substrate inhibition. In traditional Michaelis−Menten enzyme kinetics, the substrate must be present in significant excess relative to the enzyme so that the substrate concentration is not substantially reduced by formation of the enzyme−substrate complex.45 In the fluorometric assay, however, YoeBSa1 (5 μM) is present at a concentration similar to that of the fluorogenic substrate (0.5− 20 μM) in each reaction. Rather than Michaelis−Menten conditions, these enzyme and substrate concentrations resemble those of mutual depletion systems, in which formation of the enzyme−substrate complex significantly reduces the concentrations of both the enzyme and the substrate.46 Consequently, the classical Michaelis−Menten equation (eq 1) cannot be used to fit the kinetic data of YoeBSa1, but this does not necessarily mean that YoeBSa1 does not follow Michaelis−Menten kinetics. Interestingly, it has been shown that when the concentration of enzyme, [E]T, is equal to or greater than the Km, enzymes that follow Michaelis−Menten kinetics appear to have cooperative activity. The magnitude of the apparent cooperativity increases as [E]T increases relative to K m , causing a concomitant increase in the substrate concentration ([S]T)0.5 at which half-maximal velocity is observed.47 This increase is given by eq 2: ([S]T )0.5 =

[E]T + Km 2

θ=

[L]h (KA )h + [L]h

(3)

where θ is the ratio of occupied binding sites to total binding sites, [L] is the ligand concentration, KA is the association constant, and h is the Hill coefficient, which quantifies the degree of cooperativity.48 The maximum possible value of h for a perfectly cooperative protein is equal to the number of ligandbinding sites. An h >1 indicates positive cooperativity, where the rate of ligand binding is enhanced by already bound ligands. An h